The ideal seats for a couple are on a 747 - 1A and 1K so you both have windows. Can't you ask for a bigger plane?

Otherwise, as others have said, you have to choose between a window and being together. I love windows, but if the flight is entirely at night they don't make a lot of difference. Can you mix and match a bit? Choose a middle pair (2EF if possible, but I don't really think there's a lot to choose between them) on one sector and 2K/3K (or 2A/3A if you're left-handed!) on another sector, preferably a daytime one.

Perhaps it's because I've only travelled twice in F on a 777, but I can't say I think there's a lot of difference between the various rows. There's a lot more to say about the 747.